Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Mechanisms of metal sorption by biochars: Biochar characteristics and modifications

Development of Biochar-Based Functional Materials: Toward a Sustainable Platform Carbon Material

Recent advancements in supercapacitor technology

Adsorption of heavy metals on conventional and nanostructured materials for wastewater treatment purposes: A review

The enzyme Na+/K+-ATPase (NKA) is important in the heart. Reductions in NKA activity and expression have often been observed in chronic kidney disease (CKD)-related heart injury. Previously, our group found that an antibody targeting the NKA1α1 subunit’s DR extracellular region (897DVEDSYGQQWTYEQR911) stimulated NKA activities and produced cardioprotective effects against ischemic injury and isoproterenol-induced cardiac remodeling. In here, we assessed whether DRm217, a specific DR antibody, exhibits cardioprotective effects in chronic renal failure models. In 5/6 nephrectomy (5/6 Nx) surgery to mimic CKD in Sprague Dawley rat, we observed that NKA activity and expression were depressed in the hearts of 5/6 Nx rats. DRm217, an NKA DR region antibody, alleviated heart hypertrophy and cardiac fibrosis under 5/6 Nx conditions. Further studies revealed that DRm217 inhibited Src activation and reduced reactive oxygen species (ROS) levels in hearts under 5/6 Nx conditions. Our findings imply that NKA could be a treatment target in CKD-related cardiac diseases. Prevention of CKD-induced myocardial injury by DRm217 provides an appealing therapeutic alternative.

Na+/K+-ATPase DR region antibody ameliorated cardiac hypertrophy and fibrosis in rats with 5/6 nephrectomy

Glioblastoma is among the most malignant tumors in the central nervous system and characterized by strong invasion and poor prognosis. Fibronectin type III domain-containing 4 (FNDC4) plays various important roles in the human body, including participating in cellular metabolism and inflammatory responses to cardiovascular diseases, influencing immune cells, and exerting anti-inflammatory effects; however, the role of FNDC4 in glioblastoma has not been reported.In this study, bioinformatics databases, including TCGA, CGGA, GTEx, and TIMER, were used to analyze the differential expression of FNDC4 genes and cell survival, in addition to investigating its relationship with immune cell infiltration. Additionally, we overexpressed FNDC4 in glioblastoma cell lines U87 and U251 by lentiviral transfection and detected changes in proliferation, cell cycle progression, and apoptosis. Following collection of monocytes from the peripheral blood of healthy individuals and transformation into M0 macrophages, we performed flow cytometry to detect the polarizing effect of exogenous FNDC4, as well as the effect of FNDC4-overexpressing glioblastoma cells on macrophage polarization in a co-culture system.We identified that significantly higher FNDC4 expression in glioblastoma tissue relative to normal brain tissue was associated with worse prognosis. Moreover, we found that FNDC4 overexpression in U87 and U251 cells resulted in increased proliferation and affected the S phase of tumor cells, whereas cell apoptosis remained unchanged. Furthermore, exogenous FNDC4 inhibited the M1 polarization of M0 macrophages without affecting M2 polarization; this was also observed in glioblastoma cells overexpressing FNDC4.FNDC4 expression is elevated in glioblastoma, closely associated with poor prognosis, and promoted the proliferation of glioblastoma cells, affected the S phase of tumor cells while inhibiting macrophage polarization. 

/pdf/correlation-of-the-prognostic-value-of-fndc4-in-glioblastoma-slqz5nzs.pdf

Correlation of the prognostic value of FNDC4 in glioblastoma with macrophage polarization

Humic acids (HAs) widely exist in water environment, and has an important impact on the adsorption of pollutants. Herein, HAs (both dissolved and coated) was employed to assess the effect on the removal of the organic contaminant tetracycline (TC) by K2CO3 modified magnetic biochar (KMBC). Results showed that low concentration of dissolved HAs promoted TC removal, likely due to a bridging effect, while higher concentration of dissolved HAs inhibited TC adsorption because of the competition of adsorption sites on KMBC. By characterization analysis, coated HAs changed the surface and pore characteristics of KMBC, which suppressed the TC removal. In a sequential adsorption experiment involving dissolved HAs and TC, the addition of HAs at the end of the experiment led to the formation of HAs-TC ligands with free TC, which improved the adsorption capacity of TC. TC adsorption by KMBC in the presence of dissolved HAs and coated HAs showed a downward trend with increasing pH from 5.0 to 10.0. The TC adsorption process was favorable and endothermic, and could be better simulated by pseudo-second-order kinetics and Freundlich isotherm model. Hydrogen bonds and π-π interactions were hypothesized to be the underlying influencing mechanisms. 

/pdf/effect-of-dissolved-humic-acids-and-coated-humic-acids-on-1uorfgbp.pdf

Effect of dissolved humic acids and coated humic acids on tetracycline adsorption by K2CO3-activated magnetic biochar

Following the publication of this paper, the authors contacted the Editorial Office to request that the article be retracted on account of an inability to obtain consistent results from repeated experiments. Independently, it was drawn to the Editor's attention that certain of the flow cytometric data shown in Figs. 2D, 5D and 6D were strikingly similar to data appearing in different form in another article by different authors. Owing to the fact that the contentious data in the above article were already under consideration for publication prior to its submission to Oncology Reports, the Editor has agreed to the authors' request that this article should be retracted from the Journal. The Editor apologizes to the readership for any inconvenience caused. [the original article was published in Oncology Reports 40: 554‑564, 2018; DOI: 10.3892/or.2018.6449].

https://www.spandidos-publications.com/10.3892/or.2022.8274/download

MicroRNA-485 plays tumour-suppressive roles in colorectal cancer by directly targeting GAB2

The invention discloses ramie fiber-based biochar, a preparation method and application thereof. The preparation method of the ramie fiber-based biochar comprises the following steps of: taking ramiefilaments as the raw material to prepare ramie filament biochar, mixing the ramie filament biochar mixed with a deep eutectic solvent, conducting ultrasonic dispersion and carrying out hydrothermal reaction, and conducting pyrolysis carbonization on the obtained ramie fiber biochar, thus obtaining the ramie fiber-based biochar. The ramie fiber-based biochar prepared by the invention has the advantages of large specific surface area, high graphitization degree, good electron transfer performance, high catalytic activity and the like, and is a novel biochar material composed of ramie fiber structure, and the preparation method has the advantages of simple process, strong operability and the like, is suitable for large-scale preparation, and is beneficial to wide application. The ramie fiber-based biochar can be used as an activator for activating persulfate to degrade organic pollutants in water, can realize effective degradation of the organic pollutants, has the advantages of simple operation, high treatment efficiency, strong stability and the like, and has high use value and good application prospect.

Xiaofei Tan

Papers

Na+/K+-ATPase DR region antibody ameliorated cardiac hypertrophy and fibrosis in rats with 5/6 nephrectomy

Correlation of the prognostic value of FNDC4 in glioblastoma with macrophage polarization

Effect of dissolved humic acids and coated humic acids on tetracycline adsorption by K2CO3-activated magnetic biochar

MicroRNA-485 plays tumour-suppressive roles in colorectal cancer by directly targeting GAB2

Ramie fiber-based biochar, preparation method and application thereof